MDC Exchange Program in Medical Systems Biology

MDC-MRC HGU Scientific Symposium at MDC-BIMSB in December 2023

Systems biology combines molecular biology, biochemistry, computational sciences, mathematics and physics to quantitatively capture and predict complex processes of life.

The MDC Exchange Program in Medical Systems Biology (formerly called MDC-NYU Exchange Program) was launched in 2009 to train the next generation of systems biologists. Ten PhD students are able to spend up to two years working and studying at the Center for Genomics and Systems Biology at New York University or at the MRC Human Genetics Unit at University of Edinburgh. Students can also take advantage of our state of the art technology platforms and a training programme of specialist courses and personal development opportunities.

All partner institutions are committed to sharing their scientific and educational expertise with their respective student bodies.

December 2019: MDC-NYU exchange program fellows, BIMSB and NYU faculty discuss ongoing and new collaborations during the annual bilateral meeting at the Center for Genomics and Systems Biology in New York.

As of December 2019, a total of 22 MDC-NYU program fellows have co-authored 46 publications. The success of the program is highlighted by 11 joint publications with NYU faculty.

Research Training

The Berlin Institute for Medical Systems Biology offers an exceptional PhD Exchange Program to support interdisciplinary research projects and international PhD education.

PhD topics are structured as collaborative projects between MDC and New York University or University of Edinburgh. A Principal Investigator from each institution supervises students who are expected to divide their time between Berlin and New York or Edinburgh, taking advantage of complimentary research and training expertise. Resources are available for travel for short and long term working periods as well as for course and conference participation. The regular guidance of an international PhD Committee supports the creation of individual research and training portfolios.

 

Our program offers:

• interdisciplinary research training in top ranking labs
• projects that are dually mentored by a group leader from MDC and NYU/MRC HGU
• students are supported to spend up to fifty percent of their time at NYU/MRC HGU
• access to and training in high-end technologies, such as novel sequencing applications, multi-omics approaches, organoid models and bioinformatics
• an extensive and comprehensive archive of animal model systems for evo-devo or translational approaches
• participation in interdisciplinary classes, soft skills courses, student focussed seminars and specialist summer schools
• the regular opportunity to present your research at the BIMSB Student Seminar and attend the Systems Biology Lecture Series

More about PhD programmes at the MDC

More about the Center for Genomics and Systems Biology at NYU

More about the MRC Human Genetics Unit at University of Edinburgh

Student Profiles

Up to 10 interdisciplinary graduate students join the program.

Students of the MDC Exchange Program in MSB in 2024: Meghna Joon, Simone Del Giudice, Yun-Hsuan Huang, Lena Nitsch, Philipp Stachel-Braum, Philipp Roth (not in the picture)

Here we introduce the MDC-based students and their joint projects with international partners, including the student's first author publications.

Meghna Joon (2023-)

Supervisory team: Michael Robson

Yun-Hsuan Huang (2022-)

Supervisory team: Ilaria Piazza and Nick Gilbert

Philipp Roth (2021-)

Supervisory team: Jakob Metzger and Esteban Mazzoni

Philipp Stachel-Braum (2020-)

Supervisory team: Stefanie Grosswendt and Itai Yanai

Lena Nitsch (2020-)

Supervisory team: Leif Ludwig and Aristotelis Tsirigos

Isabella Douzoglou (2020-)

Supervisory team: Melissa Birol

Simone Del Giudice (2019-2025)

Supervisory team: Markus Landthaler

Miriam Wandres (2019-2024)

Supervisory team: Nikolaus Rajewsky

Peter Hirsch (2018-2023)

Supervisory team: Dagmar Kainmüller and Stephan Preibisch

Liene Astica (2018-2023)

Role of CTCF in the evolution of metazoan chromatin architecture

Supervisory team: Dario Lupianez and Robert Zinzen and Lionel Christiaen

Jonathan Alles (2017-2022)

Poly(A) tails in eukaryotic gene expression control

Supervisory team: Nikolaus Rajewsky and Carlos Carmona-Fontaine

Alles J*, Karaiskos N*, Praktiknjo SD, Grosswendt S, Wahle P, Ruffault PL, Ayoub S, Schreyer L, Boltengagen A, Birchmeier C, Zinzen R, Kocks C, Rajewsky N. (2017) Cell fixation and preservation for droplet-based single-cell transcriptomics. BMC Biol. 2017 May 19;15(1):44.

Legnini I*, Alles J*, Karaiskos N, Ayoub S, Rajewsky N. (2019) FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control. Nat Methods. 2019 Sep;16(9):879-886

Thomas Maximilian Sparks (2017-2023)

Incorporating RNA detection into Genome Architecture Mapping

Supervisory team: Ana Pombo and Richard Bonneau

Maria Stella de Biase (2017-2023)

Understanding the aetiology of intra-tumour heterogeneity and its functional consequences

Supervisory team: Roland Schwarz and Mark Siegal

Lorena Sofia Lopez Zepeda (2017-2023)

Using CRISRR screens to understand genomic regulation in a motor neuron programming model

Supervisory team: Uwe Ohler and Neville Sanjana

Laura Breimann (2016-2019)

Dissecting the role of chromosome condensation on transcription regulation in C.elegans
Supervisory team: Stephan Preibisch and Sevinc Ercan

Breimann L., Preusser F., Preibisch S. (2019) Light-microscopy methods in C.elegans research. Curr Opin Syst Biol 13: 82-92

Selman Bulut (2016-2019)

Tissue-specific ChIP-seq to Study Tissue-specificity of CHE-1-mediated Conversion and Genomic Distribution of Histone Variants
Supervisory team: Baris Tursun and Sevinc Ercan

Ana Miguel Fernandes (2014-2017)

Dynamic regulation of co-transcriptional processes during neuronal maturation
Supervisory team: Ana Pombo and Esteban O. Mazzoni

Nicolai Kastelic (2014-2019)

RNA-based regulation in pluripotency and differentiation
Supervisory team: Markus Landthaler and Esteban O. Mazzoni

Kastelic N, Landthaler M. (2017). mRNA interactome capture in mammalian cells. Methods.;126:38-43

Kamila Kutz (2014-2017)

Proteomic identification and characterization of micropeptides
Supervisory team: Matthias Selbach and Richard Bonneau

Mahmoud Ibrahim (2013-2017)

Probabilistic modeling methods to identify chromatin state transitions in time course data
Supervisory team: Uwe Ohler and Esteban O. Mazzoni

Ibrahim MM, Lacadie SA, Ohler U. (2015) JAMM: a peak finder for joint analysis of NGS replicates. Bioinformatics. 2015 Jan 1;31(1):48-55

Velasco, S.*, Ibrahim, M.M.*, Kakumanu, A., Garipler, G., Aydin, B., Al-Sayegh, M.A., Hirsekorn, A., Abdul-Rahman, F., Satija, R., Ohler, U., Mahony, S., Mazzoni, E.O. (2017). A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. Cell Stem Cell 20, 205-217.e208.

Ibrahim MM, Karabacak A, Glahs A, Kolundzic E, Hirsekorn A, Carda A, Tursun B, Zinzen RP, Lacadie SA, Ohler U. (2018) Determinants of promoter and enhancer transcription directionality in metazoans. Nat Commun. 2018 Oct 26;9(1):4472.

Panagiotis Papavasileiou (2013-2017)

Biogenesis and function of circular and other ncRNAs in development
Supervisory team: Nikolaus Rajewsky and Claude Desplan

Memczak S*, Papavasileiou P*, Peters O, Rajewsky N. (2015). Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood. PLoS One;10(10):e0141214. *equal contribution

Alessandra Zappulo (2013-2017)

Subcellular mRNA localization and translation in mESC derived neurons
Supervisory team: Marina Chekulaeva and Esteban O. Mazzoni

Zappulo, A., Van Den Bruck, D., Ciolli Mattioli, C., Franke, V., Imami, K., McShane, E., Moreno-Estelles, M., Calviello, L., Filipchyk, A., Peguero-Sanchez, E., Müller, T., Woehler, A., Birchmeier, C., Merino, E., Rajewsky, N., Ohler, U., Mazzoni, E.O., Selbach, M., Akalin, A., Chekulaeva, M. (2017). RNA localization is a key determinant of neurite-enriched proteome. Nat Commun 8, 583.

Fabian Bindel (2010-2014)

Deciphering links between transcription factor signaling and cancer metabolism
Supervisory team: Stefan Kempa and Richard Bonneau

Rohwer N*, Bindel F*, Grimm C, Lin SJ, Wappler J, Klinger B, Blüthgen N, Du Bois I, Schmeck B, Lehrach H, de Graauw M, Goncalves E, Saez-Rodriguez J, Tan P, Grabsch HI, Prigione A, Kempa S, Cramer T. (2016) Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A. Oncotarget. 2016 Feb 9;7(6):6693-710. doi: 10.18632/oncotarget.6793

Mathias Munschauer (2010-2014)

High-resolution profiling of protein-RNA interactions
Supervisory team: Markus Landthaler and Christine Vogel

Graf R*, Munschauer M*, Mastrobuoni G, Mayr F, Heinemann U, Kempa S, Rajewsky N, Landthaler M. (2013) Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation. RNA Biol. 2013 Jul;10(7):1146-59.

Schueler M*, Munschauer M*, Gregersen LH, Finzel A, Loewer A, Chen W, Landthaler M, Dieterich C. (2014) Differential protein occupancy profiling of the mRNA transcriptome. Genome Biol. 2014 Jan 13;15(1):R15.

Munschauer M, Schueler M, Dieterich C, Landthaler M. (2014) High-resolution profiling of protein occupancy on polyadenylated RNA transcripts. Methods. 2014 Feb;65(3):302-9

Munschauer M., Vogel J. (2018). Nuclear lncRNA stabilization in the host response to bacterial infection. EMBO J. 2018 Jul 2;37(13).

Martina Weigt (2010-)

Genome wide DNA CpG methylation profiling using massive parallel bisulfite sequencing
Supervisory team: Wei Chen and Fei Li

Rina Ahmed (2009-2014)

Bioinformatic analysis of microRNA genes in free-living and parasitic nematodes
Supervisory team: Christoph Dieterich and Kris Gunsalus

Ahmed R, Chang Z, Younis AE, Langnick C, Li N, Chen W, Brattig N, Dieterich C. (2013). Conserved miRNAs are candidate post-transcriptional regulators of developmental arrest in free-living and parasitic nematodes. Genome Biol Evol. 2013;5(7):1246-60.

Alexander Baltz (2009-2013)

The mRNA-bound Proteome of a human cell-line and in early Drosophila embryogenesis
Supervisory team: Markus Landthaler and Stephen Small

Baltz AG., Munschauer M., Schwanhaeusser B., Vasile A., Murakawa Y., Schueler M., Youngs N., Penfold-Brown D., Drew K., Milek M., Wyler E., Bonneau R., Selbach M., Dieterich C., Landthaler M. (2012). The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol Cell. 46 (5): 674-690

Jiaxuan Chen (2009-2015)

Analysis of protein-protein interaction during embryogenesis in C. elegans
Supervisory team: Matthias Selbach and Fabio Piano

Sury MD*, Chen JX*, Selbach M. (2010) The SILAC fly allows for accurate protein quantification in vivo. Mol Cell Proteomics. 2010 Oct;9(10):2173-83 *equal contribution

Sury MD*, Chen JX*, Selbach M. (2014) In vivo stable isotope labeling by amino acids in Drosophila melanogaster. Methods Mol Biol. ;1188:85-93. *equal contribution

Chen JX, Cipriani PG, Mecenas D, Polanowska J, Piano F, Gunsalus KC, Selbach M. (2016). In Vivo Interaction Proteomics in Caenorhabditis elegans Embryos Provides New Insights into P Granule Dynamics. Mol Cell Proteomics;15(5):1642-57

Anna-Carina Jungkamp (2009-2012)

In vivo and transcriptome-wide identification of RNA binding protein target sites
Supervisory team: Nikolaus Rajewsky and Fabio Piano

Jungkamp, A.C., Stoeckius, M., Mecenas, D., Grün, D., Mastrobuoni, G., Kempa, S., Rajewsky, N. (2011). In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites. Mol Cell. 4: 828-40

Marlon Stoeckius (2009-2011)

High resolution transcriptome and proteome profiling during oocyte to embryo transition in C.elegans
Supervisory team: Nikolaus Rajewsky and Fabio Piano

Stoeckius M., Maaskola J., Colombo T., Rahn H.P., Friedlaender M.R., Li N.; Chen W., Piano F., Rajewsky N. (2009-10). Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nature Methods 6 (10): 745-751

Stoeckius M, Grün D, Rajewsky N. (2014) Paternal RNA contributions in the Caenorhabditis elegans zygote. EMBO J. 2014 Aug 18;33(16):1740-50.

Stoeckius M., Gruen D., Kirchner M., Ayoub S., Torti F., Piano F., Herzog M., Selbach M., Rajewsky N. (2014). Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism EMBO J. 33(16): 1751-1766

 

How to Apply

You can find all details on deadlines and the application process at the MDC Graduate Office Website.

Experiences

Explore inspiring stories from past participants who gained invalueble experiences through our student exchange program.

Institute & Campus January 31, 2025

“Seize the chance– it’s worth it!”

Doctoral student Philipp Roth went to New York as part of the Max Delbrück Center Exchange Program in Medical Systems Biology. In this interview, he discusses his research collaboration with a lab at NYU and how the exchange benefitted him in ways he could not have imagined.

Institute & Campus December 08, 2023

“I gained self-confidence in New York”

Working in Berlin-Mitte and New York – Lena Nitsch conducts research at both the MDC-BIMSB and New York University. For “We at the MDC”, the doctoral student discusses how it is to work in two labs, her experiences in the United States, and what she has learned through the “MDC-NYU PhD Exchange Program”.